1 |
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#include "Integrator.hpp" |
2 |
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#include "simError.h" |
3 |
< |
#include <cmath> |
3 |
> |
#include <math.h> |
4 |
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template<typename T> ZConstraint<T>::ZConstraint(SimInfo* theInfo, ForceFields* the_ff) |
5 |
< |
: T(theInfo, the_ff), fz(NULL), |
6 |
< |
indexOfZConsMols(NULL) |
5 |
> |
: T(theInfo, the_ff), indexOfZConsMols(NULL), fz(NULL), curZPos(NULL), |
6 |
> |
fzOut(NULL), curZconsTime(0), forcePolicy(NULL) |
7 |
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{ |
8 |
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|
9 |
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//get properties from SimInfo |
10 |
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GenericData* data; |
11 |
< |
IndexData* index; |
11 |
> |
ZConsParaData* zConsParaData; |
12 |
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DoubleData* sampleTime; |
13 |
+ |
DoubleData* tolerance; |
14 |
+ |
StringData* policy; |
15 |
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StringData* filename; |
16 |
+ |
double COM[3]; |
17 |
+ |
|
18 |
+ |
//by default, the direction of constraint is z |
19 |
+ |
// 0 --> x |
20 |
+ |
// 1 --> y |
21 |
+ |
// 2 --> z |
22 |
+ |
whichDirection = 2; |
23 |
+ |
|
24 |
+ |
//estimate the force constant of harmonical potential |
25 |
+ |
double Kb = 1.986E-3 ; //in kcal/K |
26 |
|
|
27 |
< |
//retrieve index of z-constraint molecules |
28 |
< |
data = info->getProperty("zconsindex"); |
17 |
< |
if(!data) { |
27 |
> |
double halfOfLargestBox = max(info->boxL[0], max(info->boxL[1], info->boxL[2])) /2; |
28 |
> |
zForceConst = Kb * info->target_temp /(halfOfLargestBox * halfOfLargestBox); |
29 |
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|
30 |
+ |
//creat force Subtraction policy |
31 |
+ |
data = info->getProperty(ZCONSFORCEPOLICY_ID); |
32 |
+ |
if(!data){ |
33 |
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sprintf( painCave.errMsg, |
34 |
< |
"ZConstraint error: If you use an ZConstraint\n" |
35 |
< |
" , you must set index of z-constraint molecules.\n"); |
36 |
< |
painCave.isFatal = 1; |
37 |
< |
simError(); |
34 |
> |
"ZConstraint Warning: User does not set force Subtraction policy, " |
35 |
> |
"PolicyByMass is used\n"); |
36 |
> |
painCave.isFatal = 0; |
37 |
> |
simError(); |
38 |
> |
|
39 |
> |
forcePolicy = (ForceSubtractionPolicy*) new PolicyByMass(this); |
40 |
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} |
41 |
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else{ |
42 |
< |
index = dynamic_cast<IndexData*>(data); |
42 |
> |
policy = dynamic_cast<StringData*>(data); |
43 |
|
|
44 |
< |
if(!index){ |
29 |
< |
|
44 |
> |
if(!policy){ |
45 |
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sprintf( painCave.errMsg, |
46 |
< |
"ZConstraint error: Can not get property from SimInfo\n"); |
47 |
< |
painCave.isFatal = 1; |
48 |
< |
simError(); |
49 |
< |
|
46 |
> |
"ZConstraint Error: Convertion from GenericData to StringData failure, " |
47 |
> |
"PolicyByMass is used\n"); |
48 |
> |
painCave.isFatal = 0; |
49 |
> |
simError(); |
50 |
> |
|
51 |
> |
forcePolicy = (ForceSubtractionPolicy*) new PolicyByMass(this); |
52 |
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} |
53 |
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else{ |
54 |
< |
|
55 |
< |
indexOfAllZConsMols = index->getIndexData(); |
56 |
< |
|
57 |
< |
//the maximum value of index is the last one(we sorted the index data in SimSetup.cpp) |
58 |
< |
int maxIndex; |
42 |
< |
int minIndex; |
43 |
< |
int totalNumMol; |
44 |
< |
|
45 |
< |
minIndex = indexOfAllZConsMols[0]; |
46 |
< |
if(minIndex < 0){ |
54 |
> |
if(policy->getData() == "BYNUMBER") |
55 |
> |
forcePolicy = (ForceSubtractionPolicy*) new PolicyByNumber(this); |
56 |
> |
else if(policy->getData() == "BYMASS") |
57 |
> |
forcePolicy = (ForceSubtractionPolicy*) new PolicyByMass(this); |
58 |
> |
else{ |
59 |
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sprintf( painCave.errMsg, |
60 |
< |
"ZConstraint error: index is out of range\n"); |
61 |
< |
painCave.isFatal = 1; |
62 |
< |
simError(); |
63 |
< |
} |
64 |
< |
|
65 |
< |
maxIndex = indexOfAllZConsMols[indexOfAllZConsMols.size() - 1]; |
54 |
< |
|
55 |
< |
#ifndef IS_MPI |
56 |
< |
totalNumMol = nMols; |
57 |
< |
#else |
58 |
< |
totalNumMol = mpiSim->getTotNmol(); |
59 |
< |
#endif |
60 |
< |
|
61 |
< |
if(maxIndex > totalNumMol - 1){ |
62 |
< |
sprintf( painCave.errMsg, |
63 |
< |
"ZConstraint error: index is out of range\n"); |
64 |
< |
painCave.isFatal = 1; |
65 |
< |
simError(); |
66 |
< |
|
67 |
< |
} |
68 |
< |
|
60 |
> |
"ZConstraint Warning: unknown force Subtraction policy, " |
61 |
> |
"PolicyByMass is used\n"); |
62 |
> |
painCave.isFatal = 0; |
63 |
> |
simError(); |
64 |
> |
forcePolicy = (ForceSubtractionPolicy*) new PolicyByMass(this); |
65 |
> |
} |
66 |
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} |
70 |
– |
|
67 |
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} |
68 |
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|
69 |
+ |
|
70 |
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//retrieve sample time of z-contraint |
71 |
< |
data = info->getProperty("zconstime"); |
71 |
> |
data = info->getProperty(ZCONSTIME_ID); |
72 |
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|
73 |
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if(!data) { |
74 |
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|
96 |
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|
97 |
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} |
98 |
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|
102 |
– |
|
99 |
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//retrieve output filename of z force |
100 |
< |
data = info->getProperty("zconsfilename"); |
100 |
> |
data = info->getProperty(ZCONSFILENAME_ID); |
101 |
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if(!data) { |
102 |
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|
103 |
|
|
110 |
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} |
111 |
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else{ |
112 |
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|
113 |
< |
filename = dynamic_cast<StringData*>(data); |
113 |
> |
filename = dynamic_cast<StringData*>(data); |
114 |
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|
115 |
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if(!filename){ |
116 |
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|
124 |
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this->zconsOutput = filename->getData(); |
125 |
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} |
126 |
|
|
127 |
+ |
} |
128 |
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|
129 |
+ |
//retrieve tolerance for z-constraint molecuels |
130 |
+ |
data = info->getProperty(ZCONSTOL_ID); |
131 |
+ |
|
132 |
+ |
if(!data) { |
133 |
+ |
|
134 |
+ |
sprintf( painCave.errMsg, |
135 |
+ |
"ZConstraint error: can not get tolerance \n"); |
136 |
+ |
painCave.isFatal = 1; |
137 |
+ |
simError(); |
138 |
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} |
139 |
+ |
else{ |
140 |
|
|
141 |
+ |
tolerance = dynamic_cast<DoubleData*>(data); |
142 |
+ |
|
143 |
+ |
if(!tolerance){ |
144 |
+ |
|
145 |
+ |
sprintf( painCave.errMsg, |
146 |
+ |
"ZConstraint error: Can not get property from SimInfo\n"); |
147 |
+ |
painCave.isFatal = 1; |
148 |
+ |
simError(); |
149 |
+ |
|
150 |
+ |
} |
151 |
+ |
else{ |
152 |
+ |
this->zconsTol = tolerance->getData(); |
153 |
+ |
} |
154 |
+ |
|
155 |
+ |
} |
156 |
+ |
|
157 |
+ |
//retrieve index of z-constraint molecules |
158 |
+ |
data = info->getProperty(ZCONSPARADATA_ID); |
159 |
+ |
if(!data) { |
160 |
+ |
|
161 |
+ |
sprintf( painCave.errMsg, |
162 |
+ |
"ZConstraint error: If you use an ZConstraint\n" |
163 |
+ |
" , you must set index of z-constraint molecules.\n"); |
164 |
+ |
painCave.isFatal = 1; |
165 |
+ |
simError(); |
166 |
+ |
} |
167 |
+ |
else{ |
168 |
+ |
|
169 |
+ |
zConsParaData = dynamic_cast<ZConsParaData*>(data); |
170 |
+ |
|
171 |
+ |
if(!zConsParaData){ |
172 |
+ |
|
173 |
+ |
sprintf( painCave.errMsg, |
174 |
+ |
"ZConstraint error: Can not get parameters of zconstraint method from SimInfo\n"); |
175 |
+ |
painCave.isFatal = 1; |
176 |
+ |
simError(); |
177 |
+ |
|
178 |
+ |
} |
179 |
+ |
else{ |
180 |
+ |
|
181 |
+ |
parameters = zConsParaData->getData(); |
182 |
+ |
|
183 |
+ |
//check the range of zconsIndex |
184 |
+ |
//and the minimum value of index is the first one (we already sorted the data) |
185 |
+ |
//the maximum value of index is the last one |
186 |
+ |
|
187 |
+ |
int maxIndex; |
188 |
+ |
int minIndex; |
189 |
+ |
int totalNumMol; |
190 |
+ |
|
191 |
+ |
minIndex = (*parameters)[0].zconsIndex; |
192 |
+ |
if(minIndex < 0){ |
193 |
+ |
sprintf( painCave.errMsg, |
194 |
+ |
"ZConstraint error: index is out of range\n"); |
195 |
+ |
painCave.isFatal = 1; |
196 |
+ |
simError(); |
197 |
+ |
} |
198 |
+ |
|
199 |
+ |
maxIndex = (*parameters)[parameters->size() - 1].zconsIndex; |
200 |
+ |
|
201 |
+ |
#ifndef IS_MPI |
202 |
+ |
totalNumMol = nMols; |
203 |
+ |
#else |
204 |
+ |
totalNumMol = mpiSim->getTotNmol(); |
205 |
+ |
#endif |
206 |
+ |
|
207 |
+ |
if(maxIndex > totalNumMol - 1){ |
208 |
+ |
sprintf( painCave.errMsg, |
209 |
+ |
"ZConstraint error: index is out of range\n"); |
210 |
+ |
painCave.isFatal = 1; |
211 |
+ |
simError(); |
212 |
+ |
} |
213 |
+ |
|
214 |
+ |
//if user does not specify the zpos for the zconstraint molecule |
215 |
+ |
//its initial z coordinate will be used as default |
216 |
+ |
for(int i = 0; i < (int)(parameters->size()); i++){ |
217 |
+ |
|
218 |
+ |
if(!(*parameters)[i].havingZPos){ |
219 |
+ |
#ifndef IS_MPI |
220 |
+ |
for(int j = 0; j < nMols; j++){ |
221 |
+ |
if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){ |
222 |
+ |
molecules[j].getCOM(COM); |
223 |
+ |
break; |
224 |
+ |
} |
225 |
+ |
} |
226 |
+ |
#else |
227 |
+ |
//query which processor current zconstraint molecule belongs to |
228 |
+ |
int *MolToProcMap; |
229 |
+ |
int whichNode; |
230 |
+ |
|
231 |
+ |
MolToProcMap = mpiSim->getMolToProcMap(); |
232 |
+ |
whichNode = MolToProcMap[(*parameters)[i].zconsIndex]; |
233 |
+ |
|
234 |
+ |
//broadcast the zpos of current z-contraint molecule |
235 |
+ |
//the node which contain this |
236 |
+ |
|
237 |
+ |
if (worldRank == whichNode ){ |
238 |
+ |
|
239 |
+ |
for(int j = 0; j < nMols; j++) |
240 |
+ |
if (molecules[j].getGlobalIndex() == (*parameters)[i].zconsIndex){ |
241 |
+ |
molecules[j].getCOM(COM); |
242 |
+ |
break; |
243 |
+ |
} |
244 |
+ |
|
245 |
+ |
} |
246 |
+ |
|
247 |
+ |
MPI_Bcast(&COM[whichDirection], 1, MPI_DOUBLE, whichNode, MPI_COMM_WORLD); |
248 |
+ |
#endif |
249 |
+ |
|
250 |
+ |
(*parameters)[i].zPos = COM[whichDirection]; |
251 |
+ |
|
252 |
+ |
sprintf( painCave.errMsg, |
253 |
+ |
"ZConstraint warning: Does not specify zpos for z-constraint molecule " |
254 |
+ |
"initial z coornidate will be used \n"); |
255 |
+ |
painCave.isFatal = 0; |
256 |
+ |
simError(); |
257 |
+ |
|
258 |
+ |
} |
259 |
+ |
} |
260 |
+ |
|
261 |
+ |
}//end if (!zConsParaData) |
262 |
+ |
}//end if (!data) |
263 |
+ |
|
264 |
+ |
// |
265 |
|
#ifdef IS_MPI |
266 |
|
update(); |
267 |
|
#else |
268 |
|
int searchResult; |
138 |
– |
double COM[3]; |
269 |
|
|
270 |
|
for(int i = 0; i < nMols; i++){ |
271 |
|
|
275 |
|
|
276 |
|
zconsMols.push_back(&molecules[i]); |
277 |
|
massOfZConsMols.push_back(molecules[i].getTotalMass()); |
278 |
+ |
|
279 |
+ |
zPos.push_back((*parameters)[searchResult].zPos); |
280 |
+ |
// cout << "index: "<< (*parameters)[searchResult].zconsIndex |
281 |
+ |
// <<"\tzPos = " << (*parameters)[searchResult].zPos << endl; |
282 |
|
|
283 |
+ |
kz.push_back((*parameters)[searchResult]. kRatio * zForceConst); |
284 |
|
molecules[i].getCOM(COM); |
285 |
|
} |
286 |
|
else |
293 |
|
} |
294 |
|
|
295 |
|
fz = new double[zconsMols.size()]; |
296 |
+ |
curZPos = new double[zconsMols.size()]; |
297 |
|
indexOfZConsMols = new int [zconsMols.size()]; |
298 |
|
|
299 |
< |
if(!fz || !indexOfZConsMols){ |
299 |
> |
if(!fz || !curZPos || !indexOfZConsMols){ |
300 |
|
sprintf( painCave.errMsg, |
301 |
|
"Memory allocation failure in class Zconstraint\n"); |
302 |
|
painCave.isFatal = 1; |
303 |
|
simError(); |
304 |
|
} |
305 |
|
|
306 |
< |
for(int i = 0; i < zconsMols.size(); i++) |
306 |
> |
//determine the states of z-constraint molecules |
307 |
> |
for(int i = 0; i < (int)(zconsMols.size()); i++){ |
308 |
|
indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex(); |
309 |
+ |
|
310 |
+ |
zconsMols[i]->getCOM(COM); |
311 |
+ |
if (fabs(zPos[i] - COM[whichDirection]) < zconsTol) |
312 |
+ |
states.push_back(zcsFixed); |
313 |
+ |
else |
314 |
+ |
states.push_back(zcsMoving); |
315 |
+ |
} |
316 |
|
|
317 |
|
#endif |
318 |
+ |
|
319 |
+ |
//get total masss of unconstraint molecules |
320 |
+ |
double totalMassOfUncons_local; |
321 |
+ |
totalMassOfUncons_local = 0; |
322 |
+ |
|
323 |
+ |
for(int i = 0; i < (int)(unconsMols.size()); i++) |
324 |
+ |
totalMassOfUncons_local += unconsMols[i]->getTotalMass(); |
325 |
+ |
|
326 |
+ |
#ifndef IS_MPI |
327 |
+ |
totalMassOfUncons = totalMassOfUncons_local; |
328 |
+ |
#else |
329 |
+ |
MPI_Allreduce(&totalMassOfUncons_local, &totalMassOfUncons, 1, |
330 |
+ |
MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
331 |
+ |
#endif |
332 |
|
|
333 |
|
//get total number of unconstrained atoms |
334 |
|
int nUnconsAtoms_local; |
335 |
|
nUnconsAtoms_local = 0; |
336 |
< |
for(int i = 0; i < unconsMols.size(); i++) |
336 |
> |
for(int i = 0; i < (int)(unconsMols.size()); i++) |
337 |
|
nUnconsAtoms_local += unconsMols[i]->getNAtoms(); |
338 |
|
|
339 |
|
#ifndef IS_MPI |
340 |
|
totNumOfUnconsAtoms = nUnconsAtoms_local; |
341 |
|
#else |
342 |
< |
MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
343 |
< |
#endif |
342 |
> |
MPI_Allreduce(&nUnconsAtoms_local, &totNumOfUnconsAtoms, 1, |
343 |
> |
MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
344 |
> |
#endif |
345 |
|
|
346 |
< |
|
188 |
< |
|
189 |
< |
fzOut = new ZConsWriter(zconsOutput.c_str()); |
190 |
< |
|
191 |
< |
if(!fzOut){ |
192 |
< |
sprintf( painCave.errMsg, |
193 |
< |
"Memory allocation failure in class Zconstraint\n"); |
194 |
< |
painCave.isFatal = 1; |
195 |
< |
simError(); |
196 |
< |
} |
197 |
< |
|
346 |
> |
forcePolicy->update(); |
347 |
|
} |
348 |
|
|
349 |
|
template<typename T> ZConstraint<T>::~ZConstraint() |
350 |
|
{ |
351 |
|
if(fz) |
352 |
|
delete[] fz; |
353 |
+ |
|
354 |
+ |
if(curZPos) |
355 |
+ |
delete[] curZPos; |
356 |
|
|
357 |
|
if(indexOfZConsMols) |
358 |
|
delete[] indexOfZConsMols; |
359 |
|
|
360 |
|
if(fzOut) |
361 |
|
delete fzOut; |
362 |
+ |
|
363 |
+ |
if(forcePolicy) |
364 |
+ |
delete forcePolicy; |
365 |
|
} |
366 |
|
|
367 |
+ |
|
368 |
+ |
/** |
369 |
+ |
* |
370 |
+ |
*/ |
371 |
+ |
|
372 |
|
#ifdef IS_MPI |
373 |
|
template<typename T> void ZConstraint<T>::update() |
374 |
|
{ |
377 |
|
|
378 |
|
zconsMols.clear(); |
379 |
|
massOfZConsMols.clear(); |
380 |
+ |
zPos.clear(); |
381 |
+ |
kz.clear(); |
382 |
|
|
383 |
|
unconsMols.clear(); |
384 |
|
massOfUnconsMols.clear(); |
392 |
|
if(index > -1){ |
393 |
|
|
394 |
|
zconsMols.push_back(&molecules[i]); |
395 |
+ |
zPos.push_back((*parameters)[index].zPos); |
396 |
+ |
kz.push_back((*parameters)[index].kRatio * zForceConst); |
397 |
|
massOfZConsMols.push_back(molecules[i].getTotalMass()); |
398 |
|
|
399 |
|
molecules[i].getCOM(COM); |
406 |
|
|
407 |
|
} |
408 |
|
} |
409 |
+ |
|
410 |
+ |
//determine the states of z-constraint molecules |
411 |
+ |
for(int i = 0; i < (int)(zconsMols.size()); i++){ |
412 |
+ |
zconsMols[i]->getCOM(COM); |
413 |
+ |
if (fabs(zPos[i] - COM[whichDirection]) < zconsTol) |
414 |
+ |
states.push_back(zcsFixed); |
415 |
+ |
else |
416 |
+ |
states.push_back(zcsMoving); |
417 |
+ |
} |
418 |
+ |
|
419 |
|
|
420 |
|
//The reason to declare fz and indexOfZconsMols as pointer to array is |
421 |
|
// that we want to make the MPI communication simple |
422 |
|
if(fz) |
423 |
|
delete[] fz; |
424 |
+ |
|
425 |
+ |
if(curZPos) |
426 |
+ |
delete[] curZPos; |
427 |
|
|
428 |
|
if(indexOfZConsMols) |
429 |
|
delete[] indexOfZConsMols; |
430 |
|
|
431 |
|
if (zconsMols.size() > 0){ |
432 |
|
fz = new double[zconsMols.size()]; |
433 |
+ |
curZPos = new double[zconsMols.size()]; |
434 |
|
indexOfZConsMols = new int[zconsMols.size()]; |
435 |
|
|
436 |
< |
if(!fz || !indexOfZConsMols){ |
436 |
> |
if(!fz || !curZPos || !indexOfZConsMols){ |
437 |
|
sprintf( painCave.errMsg, |
438 |
|
"Memory allocation failure in class Zconstraint\n"); |
439 |
|
painCave.isFatal = 1; |
440 |
|
simError(); |
441 |
|
} |
442 |
|
|
443 |
< |
for(int i = 0; i < zconsMols.size(); i++){ |
443 |
> |
for(int i = 0; i < (int)(zconsMols.size()); i++){ |
444 |
|
indexOfZConsMols[i] = zconsMols[i]->getGlobalIndex(); |
445 |
|
} |
446 |
|
|
447 |
|
} |
448 |
|
else{ |
449 |
|
fz = NULL; |
450 |
+ |
curZPos = NULL; |
451 |
|
indexOfZConsMols = NULL; |
452 |
|
} |
453 |
|
|
454 |
+ |
// |
455 |
+ |
forcePolicy->update(); |
456 |
+ |
|
457 |
|
} |
458 |
|
|
459 |
|
#endif |
460 |
|
|
461 |
< |
/** Function Name: isZConstraintMol |
462 |
< |
** Parameter |
463 |
< |
** Molecule* mol |
464 |
< |
** Return value: |
465 |
< |
** -1, if the molecule is not z-constraint molecule, |
466 |
< |
** other non-negative values, its index in indexOfAllZConsMols vector |
461 |
> |
/** |
462 |
> |
* Function Name: isZConstraintMol |
463 |
> |
* Parameter |
464 |
> |
* Molecule* mol |
465 |
> |
* Return value: |
466 |
> |
* -1, if the molecule is not z-constraint molecule, |
467 |
> |
* other non-negative values, its index in indexOfAllZConsMols vector |
468 |
|
*/ |
469 |
|
|
470 |
|
template<typename T> int ZConstraint<T>::isZConstraintMol(Molecule* mol) |
477 |
|
index = mol->getGlobalIndex(); |
478 |
|
|
479 |
|
low = 0; |
480 |
< |
high = indexOfAllZConsMols.size() - 1; |
480 |
> |
high = parameters->size() - 1; |
481 |
|
|
482 |
|
//Binary Search (we have sorted the array) |
483 |
|
while(low <= high){ |
484 |
|
mid = (low + high) /2; |
485 |
< |
if (indexOfAllZConsMols[mid] == index) |
485 |
> |
if ((*parameters)[mid].zconsIndex == index) |
486 |
|
return mid; |
487 |
< |
else if (indexOfAllZConsMols[mid] > index ) |
487 |
> |
else if ((*parameters)[mid].zconsIndex > index ) |
488 |
|
high = mid -1; |
489 |
|
else |
490 |
|
low = mid + 1; |
493 |
|
return -1; |
494 |
|
} |
495 |
|
|
313 |
– |
/** |
314 |
– |
* Description: |
315 |
– |
* Reset the z coordinates |
316 |
– |
*/ |
496 |
|
template<typename T> void ZConstraint<T>::integrate(){ |
497 |
+ |
|
498 |
+ |
// creat zconsWriter |
499 |
+ |
fzOut = new ZConsWriter(zconsOutput.c_str(), parameters); |
500 |
|
|
501 |
+ |
if(!fzOut){ |
502 |
+ |
sprintf( painCave.errMsg, |
503 |
+ |
"Memory allocation failure in class Zconstraint\n"); |
504 |
+ |
painCave.isFatal = 1; |
505 |
+ |
simError(); |
506 |
+ |
} |
507 |
+ |
|
508 |
|
//zero out the velocities of center of mass of unconstrained molecules |
509 |
|
//and the velocities of center of mass of every single z-constrained molecueles |
510 |
|
zeroOutVel(); |
511 |
+ |
|
512 |
+ |
curZconsTime = zconsTime + info->getTime(); |
513 |
|
|
514 |
|
T::integrate(); |
515 |
|
|
521 |
|
* |
522 |
|
* |
523 |
|
* |
524 |
< |
*/ |
334 |
< |
|
335 |
< |
|
524 |
> |
*/ |
525 |
|
template<typename T> void ZConstraint<T>::calcForce(int calcPot, int calcStress){ |
526 |
+ |
double zsys; |
527 |
+ |
double COM[3]; |
528 |
+ |
double force[3]; |
529 |
+ |
double zSysCOMVel; |
530 |
|
|
531 |
|
T::calcForce(calcPot, calcStress); |
532 |
|
|
533 |
< |
if (checkZConsState()) |
534 |
< |
zeroOutVel(); |
533 |
> |
if (checkZConsState()){ |
534 |
> |
zeroOutVel(); |
535 |
> |
forcePolicy->update(); |
536 |
> |
} |
537 |
> |
|
538 |
> |
zsys = calcZSys(); |
539 |
> |
zSysCOMVel = calcSysCOMVel(); |
540 |
> |
#ifdef IS_MPI |
541 |
> |
if(worldRank == 0){ |
542 |
> |
#endif |
543 |
> |
//cout << "---------------------------------------------------------------------" <<endl; |
544 |
> |
//cout << "current time: " << info->getTime() << endl; |
545 |
> |
//cout << "center of mass at z: " << zsys << endl; |
546 |
> |
//cout << "before calcForce, the COMVel of system is " << zSysCOMVel <<endl; |
547 |
|
|
548 |
+ |
#ifdef IS_MPI |
549 |
+ |
} |
550 |
+ |
#endif |
551 |
+ |
|
552 |
|
//do zconstraint force; |
553 |
|
if (haveFixedZMols()) |
554 |
|
this->doZconstraintForce(); |
555 |
< |
|
555 |
> |
|
556 |
|
//use harmonical poteintial to move the molecules to the specified positions |
557 |
|
if (haveMovingZMols()) |
558 |
< |
//this->doHarmonic(); |
559 |
< |
|
560 |
< |
fzOut->writeFZ(info->getTime(), zconsMols.size(),indexOfZConsMols, fz); |
561 |
< |
|
558 |
> |
this->doHarmonic(); |
559 |
> |
|
560 |
> |
//write out forces and current positions of z-constraint molecules |
561 |
> |
if(info->getTime() >= curZconsTime){ |
562 |
> |
for(int i = 0; i < (int)(zconsMols.size()); i++){ |
563 |
> |
zconsMols[i]->getCOM(COM); |
564 |
> |
curZPos[i] = COM[whichDirection]; |
565 |
> |
|
566 |
> |
//if the z-constraint molecule is still moving, just record its force |
567 |
> |
if(states[i] == zcsMoving){ |
568 |
> |
fz[i] = 0; |
569 |
> |
Atom** movingZAtoms; |
570 |
> |
movingZAtoms = zconsMols[i]->getMyAtoms(); |
571 |
> |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
572 |
> |
movingZAtoms[j]->getFrc(force); |
573 |
> |
fz[i] += force[whichDirection]; |
574 |
> |
} |
575 |
> |
} |
576 |
> |
} |
577 |
> |
fzOut->writeFZ(info->getTime(), zconsMols.size(), indexOfZConsMols, fz, curZPos); |
578 |
> |
curZconsTime += zconsTime; |
579 |
> |
} |
580 |
> |
|
581 |
> |
zSysCOMVel = calcSysCOMVel(); |
582 |
> |
#ifdef IS_MPI |
583 |
> |
if(worldRank == 0){ |
584 |
> |
#endif |
585 |
> |
//cout << "after calcForce, the COMVel of system is " << zSysCOMVel <<endl; |
586 |
> |
#ifdef IS_MPI |
587 |
> |
} |
588 |
> |
#endif |
589 |
|
} |
590 |
+ |
|
591 |
+ |
|
592 |
+ |
/** |
593 |
+ |
* |
594 |
+ |
*/ |
595 |
|
|
596 |
|
template<typename T> double ZConstraint<T>::calcZSys() |
597 |
|
{ |
600 |
|
double totalMass; |
601 |
|
double totalMZ_local; |
602 |
|
double totalMZ; |
362 |
– |
double massOfUncons_local; |
603 |
|
double massOfCurMol; |
604 |
|
double COM[3]; |
605 |
|
|
606 |
|
totalMass_local = 0; |
367 |
– |
totalMass = 0; |
607 |
|
totalMZ_local = 0; |
369 |
– |
totalMZ = 0; |
370 |
– |
massOfUncons_local = 0; |
371 |
– |
|
608 |
|
|
609 |
|
for(int i = 0; i < nMols; i++){ |
610 |
|
massOfCurMol = molecules[i].getTotalMass(); |
612 |
|
|
613 |
|
totalMass_local += massOfCurMol; |
614 |
|
totalMZ_local += massOfCurMol * COM[whichDirection]; |
615 |
< |
|
380 |
< |
if(isZConstraintMol(&molecules[i]) == -1){ |
381 |
< |
|
382 |
< |
massOfUncons_local += massOfCurMol; |
383 |
< |
} |
384 |
< |
|
615 |
> |
|
616 |
|
} |
617 |
+ |
|
618 |
|
|
387 |
– |
|
619 |
|
#ifdef IS_MPI |
620 |
< |
MPI_Allreduce(&totalMass_local, &totalMass, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
621 |
< |
MPI_Allreduce(&totalMZ_local, &totalMZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
622 |
< |
MPI_Allreduce(&massOfUncons_local, &totalMassOfUncons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
623 |
< |
#else |
620 |
> |
MPI_Allreduce(&totalMass_local, &totalMass, 1, |
621 |
> |
MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
622 |
> |
MPI_Allreduce(&totalMZ_local, &totalMZ, 1, |
623 |
> |
MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD); |
624 |
> |
#else |
625 |
|
totalMass = totalMass_local; |
626 |
|
totalMZ = totalMZ_local; |
627 |
< |
totalMassOfUncons = massOfUncons_local; |
396 |
< |
#endif |
627 |
> |
#endif |
628 |
|
|
629 |
|
double zsys; |
630 |
|
zsys = totalMZ / totalMass; |
643 |
|
|
644 |
|
/** |
645 |
|
* |
415 |
– |
* |
416 |
– |
* |
646 |
|
*/ |
647 |
|
|
648 |
|
template<typename T> void ZConstraint<T>::zeroOutVel(){ |
650 |
|
Atom** fixedZAtoms; |
651 |
|
double COMvel[3]; |
652 |
|
double vel[3]; |
653 |
< |
|
653 |
> |
double zSysCOMVel; |
654 |
> |
|
655 |
|
//zero out the velocities of center of mass of fixed z-constrained molecules |
656 |
|
|
657 |
< |
for(int i = 0; i < zconsMols.size(); i++){ |
657 |
> |
for(int i = 0; i < (int)(zconsMols.size()); i++){ |
658 |
|
|
659 |
< |
if (states[i] == zcsFixed){ |
659 |
> |
if (states[i] == zcsFixed){ |
660 |
|
|
661 |
< |
zconsMols[i]->getCOMvel(COMvel); |
661 |
> |
zconsMols[i]->getCOMvel(COMvel); |
662 |
> |
//cout << "before resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl; |
663 |
> |
|
664 |
|
fixedZAtoms = zconsMols[i]->getMyAtoms(); |
665 |
< |
|
665 |
> |
|
666 |
|
for(int j =0; j < zconsMols[i]->getNAtoms(); j++){ |
667 |
|
fixedZAtoms[j]->getVel(vel); |
668 |
< |
vel[whichDirection] -= COMvel[whichDirection]; |
669 |
< |
fixedZAtoms[j]->setVel(vel); |
668 |
> |
vel[whichDirection] -= COMvel[whichDirection]; |
669 |
> |
fixedZAtoms[j]->setVel(vel); |
670 |
|
} |
671 |
< |
|
671 |
> |
|
672 |
> |
zconsMols[i]->getCOMvel(COMvel); |
673 |
> |
//cout << "after resetting " << indexOfZConsMols[i] <<"'s vz is " << COMvel[whichDirection] << endl; |
674 |
|
} |
441 |
– |
|
442 |
– |
} |
675 |
|
|
676 |
+ |
} |
677 |
+ |
|
678 |
+ |
//cout << "before resetting the COMVel of moving molecules is " << calcMovingMolsCOMVel() <<endl; |
679 |
+ |
|
680 |
+ |
zSysCOMVel = calcSysCOMVel(); |
681 |
+ |
#ifdef IS_MPI |
682 |
+ |
if(worldRank == 0){ |
683 |
+ |
#endif |
684 |
+ |
//cout << "before resetting the COMVel of sytem is " << zSysCOMVel << endl; |
685 |
+ |
#ifdef IS_MPI |
686 |
+ |
} |
687 |
+ |
#endif |
688 |
+ |
|
689 |
|
// calculate the vz of center of mass of unconstrained molecules and moving z-constrained molecules |
690 |
|
double MVzOfMovingMols_local; |
691 |
|
double MVzOfMovingMols; |
695 |
|
MVzOfMovingMols_local = 0; |
696 |
|
totalMassOfMovingZMols_local = 0; |
697 |
|
|
698 |
< |
for(int i =0; i < unconsMols.size(); i++){ |
698 |
> |
for(int i =0; i < (int)(unconsMols.size()); i++){ |
699 |
|
unconsMols[i]->getCOMvel(COMvel); |
700 |
|
MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection]; |
701 |
|
} |
702 |
|
|
703 |
< |
for(int i = 0; i < zconsMols[i]->getNAtoms(); i++){ |
459 |
< |
|
703 |
> |
for(int i = 0; i < (int)(zconsMols.size()); i++){ |
704 |
|
if (states[i] == zcsMoving){ |
705 |
|
zconsMols[i]->getCOMvel(COMvel); |
706 |
|
MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection]; |
707 |
< |
totalMassOfMovingZMols_local += massOfZConsMols[i]; |
707 |
> |
totalMassOfMovingZMols_local += massOfZConsMols[i]; |
708 |
|
} |
709 |
< |
|
709 |
> |
|
710 |
|
} |
711 |
|
|
712 |
|
#ifndef IS_MPI |
722 |
|
|
723 |
|
//modify the velocites of unconstrained molecules |
724 |
|
Atom** unconsAtoms; |
725 |
< |
for(int i = 0; i < unconsMols.size(); i++){ |
725 |
> |
for(int i = 0; i < (int)(unconsMols.size()); i++){ |
726 |
|
|
727 |
|
unconsAtoms = unconsMols[i]->getMyAtoms(); |
728 |
|
for(int j = 0; j < unconsMols[i]->getNAtoms();j++){ |
735 |
|
|
736 |
|
//modify the velocities of moving z-constrained molecuels |
737 |
|
Atom** movingZAtoms; |
738 |
< |
for(int i = 0; i < zconsMols[i]->getNAtoms(); i++){ |
738 |
> |
for(int i = 0; i < (int)(zconsMols.size()); i++){ |
739 |
|
|
740 |
|
if (states[i] ==zcsMoving){ |
741 |
|
|
742 |
|
movingZAtoms = zconsMols[i]->getMyAtoms(); |
743 |
< |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
743 |
> |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
744 |
|
movingZAtoms[j]->getVel(vel); |
745 |
|
vel[whichDirection] -= vzOfMovingMols; |
746 |
< |
movingZAtoms[j]->setVel(vel); |
503 |
< |
} |
504 |
< |
|
746 |
> |
movingZAtoms[j]->setVel(vel); |
747 |
|
} |
748 |
+ |
|
749 |
+ |
} |
750 |
|
|
751 |
+ |
} |
752 |
+ |
|
753 |
+ |
|
754 |
+ |
zSysCOMVel = calcSysCOMVel(); |
755 |
+ |
#ifdef IS_MPI |
756 |
+ |
if(worldRank == 0){ |
757 |
+ |
#endif |
758 |
+ |
//cout << "after resetting the COMVel of moving molecules is " << zSysCOMVel << endl; |
759 |
+ |
#ifdef IS_MPI |
760 |
|
} |
761 |
+ |
#endif |
762 |
|
|
763 |
|
} |
764 |
|
|
765 |
+ |
/** |
766 |
+ |
* |
767 |
+ |
*/ |
768 |
+ |
|
769 |
|
template<typename T> void ZConstraint<T>::doZconstraintForce(){ |
770 |
|
|
771 |
|
Atom** zconsAtoms; |
772 |
|
double totalFZ; |
773 |
|
double totalFZ_local; |
516 |
– |
double COMvel[3]; |
774 |
|
double COM[3]; |
775 |
|
double force[3]; |
519 |
– |
double zsys; |
776 |
|
|
777 |
< |
int nMovingZMols_local; |
522 |
< |
int nMovingZMols; |
523 |
< |
|
524 |
< |
//constrain the molecules which do not reach the specified positions |
525 |
< |
|
526 |
< |
zsys = calcZSys(); |
527 |
< |
cout <<"current time: " << info->getTime() <<"\tcenter of mass at z: " << zsys << endl; |
777 |
> |
//constrain the molecules which do not reach the specified positions |
778 |
|
|
779 |
|
//Zero Out the force of z-contrained molecules |
780 |
|
totalFZ_local = 0; |
781 |
|
|
782 |
|
//calculate the total z-contrained force of fixed z-contrained molecules |
783 |
< |
for(int i = 0; i < zconsMols.size(); i++){ |
784 |
< |
|
783 |
> |
|
784 |
> |
//cout << "before zero out z-constraint force on fixed z-constraint molecuels " |
785 |
> |
// << "total force is " << calcTotalForce() << endl; |
786 |
> |
|
787 |
> |
for(int i = 0; i < (int)(zconsMols.size()); i++){ |
788 |
> |
|
789 |
|
if (states[i] == zcsFixed){ |
790 |
< |
|
790 |
> |
|
791 |
|
zconsMols[i]->getCOM(COM); |
792 |
|
zconsAtoms = zconsMols[i]->getMyAtoms(); |
793 |
|
|
795 |
|
for(int j =0; j < zconsMols[i]->getNAtoms(); j++) { |
796 |
|
zconsAtoms[j]->getFrc(force); |
797 |
|
fz[i] += force[whichDirection]; |
798 |
< |
} |
798 |
> |
} |
799 |
|
totalFZ_local += fz[i]; |
800 |
|
|
801 |
< |
cout << "index: " << indexOfZConsMols[i] <<"\tcurrent zpos: " << COM[whichDirection] << endl; |
801 |
> |
//cout << "Fixed Molecule\tindex: " << indexOfZConsMols[i] |
802 |
> |
// <<"\tcurrent zpos: " << COM[whichDirection] |
803 |
> |
// << "\tcurrent fz: " <<fz[i] << endl; |
804 |
|
|
805 |
+ |
|
806 |
|
} |
807 |
< |
|
807 |
> |
|
808 |
|
} |
809 |
|
|
810 |
< |
//calculate the number of atoms of moving z-constrained molecules |
554 |
< |
nMovingZMols_local = 0; |
555 |
< |
for(int i = 0; zconsMols.size(); i++){ |
556 |
< |
if(states[i] == zcsMoving) |
557 |
< |
nMovingZMols_local += massOfZConsMols[i]; |
558 |
< |
} |
810 |
> |
//calculate total z-constraint force |
811 |
|
#ifdef IS_MPI |
812 |
|
MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
561 |
– |
MPI_Allreduce(&nMovingZMols_local, &nMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
813 |
|
#else |
814 |
|
totalFZ = totalFZ_local; |
564 |
– |
nMovingZMols = nMovingZMols_local; |
815 |
|
#endif |
816 |
|
|
817 |
+ |
|
818 |
+ |
// apply negative to fixed z-constrained molecues; |
819 |
|
force[0]= 0; |
820 |
|
force[1]= 0; |
821 |
|
force[2]= 0; |
570 |
– |
force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZMols); |
822 |
|
|
823 |
< |
//modify the velocites of unconstrained molecules |
824 |
< |
for(int i = 0; i < unconsMols.size(); i++){ |
823 |
> |
for(int i = 0; i < (int)(zconsMols.size()); i++){ |
824 |
> |
|
825 |
> |
if (states[i] == zcsFixed){ |
826 |
> |
|
827 |
> |
int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms(); |
828 |
> |
zconsAtoms = zconsMols[i]->getMyAtoms(); |
829 |
> |
|
830 |
> |
for(int j =0; j < nAtomOfCurZConsMol; j++) { |
831 |
> |
//force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol; |
832 |
> |
force[whichDirection] = - forcePolicy->getZFOfFixedZMols(zconsMols[i], zconsAtoms[j], fz[i]); |
833 |
> |
zconsAtoms[j]->addFrc(force); |
834 |
> |
} |
835 |
> |
|
836 |
> |
} |
837 |
> |
|
838 |
> |
} |
839 |
> |
|
840 |
> |
//cout << "after zero out z-constraint force on fixed z-constraint molecuels " |
841 |
> |
// << "total force is " << calcTotalForce() << endl; |
842 |
> |
|
843 |
> |
|
844 |
> |
force[0]= 0; |
845 |
> |
force[1]= 0; |
846 |
> |
force[2]= 0; |
847 |
> |
|
848 |
> |
//modify the forces of unconstrained molecules |
849 |
> |
for(int i = 0; i < (int)(unconsMols.size()); i++){ |
850 |
|
|
851 |
|
Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); |
852 |
|
|
853 |
< |
for(int j = 0; j < unconsMols[i]->getNAtoms(); j++) |
853 |
> |
for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){ |
854 |
> |
//force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms); |
855 |
> |
force[whichDirection] = forcePolicy->getZFOfMovingMols(unconsAtoms[j],totalFZ); |
856 |
|
unconsAtoms[j]->addFrc(force); |
857 |
+ |
} |
858 |
|
|
859 |
|
} |
860 |
|
|
861 |
< |
//modify the velocities of moving z-constrained molecules |
862 |
< |
for(int i = 0; i < zconsMols.size(); i++) { |
863 |
< |
if (states[i] == zcsMoving){ |
864 |
< |
|
865 |
< |
Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
861 |
> |
//modify the forces of moving z-constrained molecules |
862 |
> |
for(int i = 0; i < (int)(zconsMols.size()); i++) { |
863 |
> |
if (states[i] == zcsMoving){ |
864 |
> |
|
865 |
> |
Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
866 |
|
|
867 |
< |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++) |
868 |
< |
movingZAtoms[j]->addFrc(force); |
869 |
< |
} |
867 |
> |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
868 |
> |
//force[whichDirection] = totalFZ / (totNumOfUnconsAtoms + nMovingZAtoms); |
869 |
> |
force[whichDirection] = forcePolicy->getZFOfMovingMols(movingZAtoms[j],totalFZ); |
870 |
> |
movingZAtoms[j]->addFrc(force); |
871 |
> |
} |
872 |
> |
} |
873 |
|
} |
874 |
+ |
// cout << "after substracting z-constraint force from moving molecuels " |
875 |
+ |
// << "total force is " << calcTotalForce() << endl; |
876 |
|
|
877 |
< |
// apply negative to fixed z-constrained molecues; |
877 |
> |
} |
878 |
> |
|
879 |
> |
/** |
880 |
> |
* |
881 |
> |
* |
882 |
> |
*/ |
883 |
> |
|
884 |
> |
template<typename T> void ZConstraint<T>::doHarmonic(){ |
885 |
> |
double force[3]; |
886 |
> |
double harmonicU; |
887 |
> |
double harmonicF; |
888 |
> |
double COM[3]; |
889 |
> |
double diff; |
890 |
> |
double totalFZ_local; |
891 |
> |
double totalFZ; |
892 |
> |
|
893 |
> |
force[0] = 0; |
894 |
> |
force[1] = 0; |
895 |
> |
force[2] = 0; |
896 |
> |
|
897 |
> |
totalFZ_local = 0; |
898 |
> |
|
899 |
> |
for(int i = 0; i < (int)(zconsMols.size()); i++) { |
900 |
> |
|
901 |
> |
if (states[i] == zcsMoving){ |
902 |
> |
zconsMols[i]->getCOM(COM); |
903 |
> |
// cout << "Moving Molecule\tindex: " << indexOfZConsMols[i] |
904 |
> |
// << "\tcurrent zpos: " << COM[whichDirection] << endl; |
905 |
> |
|
906 |
> |
diff = COM[whichDirection] -zPos[i]; |
907 |
> |
|
908 |
> |
harmonicU = 0.5 * kz[i] * diff * diff; |
909 |
> |
info->lrPot += harmonicU; |
910 |
> |
|
911 |
> |
harmonicF = - kz[i] * diff; |
912 |
> |
totalFZ_local += harmonicF; |
913 |
> |
|
914 |
> |
//adjust force |
915 |
> |
|
916 |
> |
Atom** movingZAtoms = zconsMols[i]->getMyAtoms(); |
917 |
> |
|
918 |
> |
for(int j = 0; j < zconsMols[i]->getNAtoms(); j++){ |
919 |
> |
//force[whichDirection] = harmonicF / zconsMols[i]->getNAtoms(); |
920 |
> |
force[whichDirection] = forcePolicy->getHFOfFixedZMols(zconsMols[i], movingZAtoms[j], harmonicF); |
921 |
> |
movingZAtoms[j]->addFrc(force); |
922 |
> |
} |
923 |
> |
} |
924 |
> |
|
925 |
> |
} |
926 |
> |
|
927 |
> |
#ifndef IS_MPI |
928 |
> |
totalFZ = totalFZ_local; |
929 |
> |
#else |
930 |
> |
MPI_Allreduce(&totalFZ_local, &totalFZ, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
931 |
> |
#endif |
932 |
> |
|
933 |
> |
//cout << "before substracting harmonic force from moving molecuels " |
934 |
> |
// << "total force is " << calcTotalForce() << endl; |
935 |
> |
|
936 |
|
force[0]= 0; |
937 |
|
force[1]= 0; |
938 |
|
force[2]= 0; |
939 |
|
|
940 |
< |
for(int i = 0; i < zconsMols.size(); i++){ |
940 |
> |
//modify the forces of unconstrained molecules |
941 |
> |
for(int i = 0; i < (int)(unconsMols.size()); i++){ |
942 |
> |
|
943 |
> |
Atom** unconsAtoms = unconsMols[i]->getMyAtoms(); |
944 |
> |
|
945 |
> |
for(int j = 0; j < unconsMols[i]->getNAtoms(); j++){ |
946 |
> |
//force[whichDirection] = - totalFZ /totNumOfUnconsAtoms; |
947 |
> |
force[whichDirection] = - forcePolicy->getHFOfUnconsMols(unconsAtoms[j], totalFZ); |
948 |
> |
unconsAtoms[j]->addFrc(force); |
949 |
> |
} |
950 |
> |
} |
951 |
|
|
952 |
< |
if (states[i] == zcsFixed){ |
953 |
< |
|
602 |
< |
int nAtomOfCurZConsMol = zconsMols[i]->getNAtoms(); |
603 |
< |
zconsAtoms = zconsMols[i]->getMyAtoms(); |
604 |
< |
|
605 |
< |
for(int j =0; j < nAtomOfCurZConsMol; j++) { |
606 |
< |
force[whichDirection] = -fz[i]/ nAtomOfCurZConsMol; |
607 |
< |
zconsAtoms[j]->addFrc(force); |
608 |
< |
} |
609 |
< |
|
610 |
< |
} |
611 |
< |
|
612 |
< |
} |
952 |
> |
//cout << "after substracting harmonic force from moving molecuels " |
953 |
> |
// << "total force is " << calcTotalForce() << endl; |
954 |
|
|
955 |
|
} |
956 |
|
|
957 |
+ |
/** |
958 |
+ |
* |
959 |
+ |
*/ |
960 |
+ |
|
961 |
|
template<typename T> bool ZConstraint<T>::checkZConsState(){ |
962 |
|
double COM[3]; |
963 |
|
double diff; |
964 |
|
|
965 |
< |
bool changed; |
965 |
> |
int changed_local; |
966 |
> |
int changed; |
967 |
|
|
968 |
< |
changed = false; |
968 |
> |
changed_local = 0; |
969 |
|
|
970 |
< |
for(int i =0; i < zconsMols.size(); i++){ |
970 |
> |
for(int i =0; i < (int)(zconsMols.size()); i++){ |
971 |
|
|
972 |
|
zconsMols[i]->getCOM(COM); |
973 |
< |
diff = fabs(COM[whichDirection] - ZPos[i]); |
974 |
< |
if ( diff <= ztol && states[i] == zcsMoving){ |
973 |
> |
diff = fabs(COM[whichDirection] - zPos[i]); |
974 |
> |
if ( diff <= zconsTol && states[i] == zcsMoving){ |
975 |
|
states[i] = zcsFixed; |
976 |
< |
changed = true; |
976 |
> |
changed_local = 1; |
977 |
|
} |
978 |
< |
else if ( diff > ztol && states[i] == zcsFixed){ |
978 |
> |
else if ( diff > zconsTol && states[i] == zcsFixed){ |
979 |
|
states[i] = zcsMoving; |
980 |
< |
changed = true; |
980 |
> |
changed_local = 1; |
981 |
|
} |
982 |
|
|
983 |
|
} |
984 |
|
|
985 |
< |
return changed; |
985 |
> |
#ifndef IS_MPI |
986 |
> |
changed =changed_local; |
987 |
> |
#else |
988 |
> |
MPI_Allreduce(&changed_local, &changed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
989 |
> |
#endif |
990 |
> |
|
991 |
> |
return (changed > 0); |
992 |
> |
|
993 |
|
} |
994 |
|
|
995 |
|
template<typename T> bool ZConstraint<T>::haveFixedZMols(){ |
643 |
– |
for(int i = 0; i < zconsMols.size(); i++) |
644 |
– |
if (states[i] == zcsFixed) |
645 |
– |
return true; |
996 |
|
|
997 |
< |
return false; |
997 |
> |
int havingFixed_local; |
998 |
> |
int havingFixed; |
999 |
> |
|
1000 |
> |
havingFixed_local = 0; |
1001 |
> |
|
1002 |
> |
for(int i = 0; i < (int)(zconsMols.size()); i++) |
1003 |
> |
if (states[i] == zcsFixed){ |
1004 |
> |
havingFixed_local = 1; |
1005 |
> |
break; |
1006 |
> |
} |
1007 |
> |
|
1008 |
> |
#ifndef IS_MPI |
1009 |
> |
havingFixed = havingFixed_local; |
1010 |
> |
#else |
1011 |
> |
MPI_Allreduce(&havingFixed_local, &havingFixed, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
1012 |
> |
#endif |
1013 |
> |
|
1014 |
> |
return (havingFixed > 0); |
1015 |
|
} |
1016 |
|
|
1017 |
|
|
1019 |
|
* |
1020 |
|
*/ |
1021 |
|
template<typename T> bool ZConstraint<T>::haveMovingZMols(){ |
655 |
– |
for(int i = 0; i < zconsMols.size(); i++) |
656 |
– |
if (states[i] == zcsMoving) |
657 |
– |
return true; |
1022 |
|
|
1023 |
< |
return false; |
1023 |
> |
int havingMoving_local; |
1024 |
> |
int havingMoving; |
1025 |
> |
|
1026 |
> |
havingMoving_local = 0; |
1027 |
> |
|
1028 |
> |
for(int i = 0; i < (int)(zconsMols.size()); i++) |
1029 |
> |
if (states[i] == zcsMoving){ |
1030 |
> |
havingMoving_local = 1; |
1031 |
> |
break; |
1032 |
> |
} |
1033 |
> |
|
1034 |
> |
#ifndef IS_MPI |
1035 |
> |
havingMoving = havingMoving_local; |
1036 |
> |
#else |
1037 |
> |
MPI_Allreduce(&havingMoving_local, &havingMoving, 1, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
1038 |
> |
#endif |
1039 |
> |
|
1040 |
> |
return (havingMoving > 0); |
1041 |
|
|
1042 |
< |
} |
1042 |
> |
} |
1043 |
> |
|
1044 |
> |
/** |
1045 |
> |
* |
1046 |
> |
*/ |
1047 |
> |
|
1048 |
> |
template<typename T> double ZConstraint<T>::calcMovingMolsCOMVel() |
1049 |
> |
{ |
1050 |
> |
double MVzOfMovingMols_local; |
1051 |
> |
double MVzOfMovingMols; |
1052 |
> |
double totalMassOfMovingZMols_local; |
1053 |
> |
double totalMassOfMovingZMols; |
1054 |
> |
double COMvel[3]; |
1055 |
> |
|
1056 |
> |
MVzOfMovingMols_local = 0; |
1057 |
> |
totalMassOfMovingZMols_local = 0; |
1058 |
> |
|
1059 |
> |
for(int i =0; i < unconsMols.size(); i++){ |
1060 |
> |
unconsMols[i]->getCOMvel(COMvel); |
1061 |
> |
MVzOfMovingMols_local += massOfUnconsMols[i] * COMvel[whichDirection]; |
1062 |
> |
} |
1063 |
> |
|
1064 |
> |
for(int i = 0; i < zconsMols.size(); i++){ |
1065 |
> |
|
1066 |
> |
if (states[i] == zcsMoving){ |
1067 |
> |
zconsMols[i]->getCOMvel(COMvel); |
1068 |
> |
MVzOfMovingMols_local += massOfZConsMols[i] * COMvel[whichDirection]; |
1069 |
> |
totalMassOfMovingZMols_local += massOfZConsMols[i]; |
1070 |
> |
} |
1071 |
> |
|
1072 |
> |
} |
1073 |
> |
|
1074 |
> |
#ifndef IS_MPI |
1075 |
> |
MVzOfMovingMols = MVzOfMovingMols_local; |
1076 |
> |
totalMassOfMovingZMols = totalMassOfMovingZMols_local; |
1077 |
> |
#else |
1078 |
> |
MPI_Allreduce(&MVzOfMovingMols_local, &MVzOfMovingMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1079 |
> |
MPI_Allreduce(&totalMassOfMovingZMols_local, &totalMassOfMovingZMols, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1080 |
> |
#endif |
1081 |
> |
|
1082 |
> |
double vzOfMovingMols; |
1083 |
> |
vzOfMovingMols = MVzOfMovingMols / (totalMassOfUncons + totalMassOfMovingZMols); |
1084 |
> |
|
1085 |
> |
return vzOfMovingMols; |
1086 |
> |
} |
1087 |
> |
|
1088 |
> |
/** |
1089 |
> |
* |
1090 |
> |
*/ |
1091 |
> |
|
1092 |
> |
template<typename T> double ZConstraint<T>::calcSysCOMVel() |
1093 |
> |
{ |
1094 |
> |
double COMvel[3]; |
1095 |
> |
double tempMVz_local; |
1096 |
> |
double tempMVz; |
1097 |
> |
double massOfZCons_local; |
1098 |
> |
double massOfZCons; |
1099 |
> |
|
1100 |
> |
|
1101 |
> |
tempMVz_local = 0; |
1102 |
> |
|
1103 |
> |
for(int i =0 ; i < nMols; i++){ |
1104 |
> |
molecules[i].getCOMvel(COMvel); |
1105 |
> |
tempMVz_local += molecules[i].getTotalMass()*COMvel[whichDirection]; |
1106 |
> |
} |
1107 |
> |
|
1108 |
> |
massOfZCons_local = 0; |
1109 |
> |
|
1110 |
> |
for(int i = 0; i < (int)(massOfZConsMols.size()); i++){ |
1111 |
> |
massOfZCons_local += massOfZConsMols[i]; |
1112 |
> |
} |
1113 |
> |
#ifndef IS_MPI |
1114 |
> |
massOfZCons = massOfZCons_local; |
1115 |
> |
tempMVz = tempMVz_local; |
1116 |
> |
#else |
1117 |
> |
MPI_Allreduce(&massOfZCons_local, &massOfZCons, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1118 |
> |
MPI_Allreduce(&tempMVz_local, &tempMVz, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1119 |
> |
#endif |
1120 |
> |
|
1121 |
> |
return tempMVz /(totalMassOfUncons + massOfZCons); |
1122 |
> |
} |
1123 |
> |
|
1124 |
> |
/** |
1125 |
> |
* |
1126 |
> |
*/ |
1127 |
> |
|
1128 |
> |
template<typename T> double ZConstraint<T>::calcTotalForce(){ |
1129 |
> |
|
1130 |
> |
double force[3]; |
1131 |
> |
double totalForce_local; |
1132 |
> |
double totalForce; |
1133 |
> |
|
1134 |
> |
totalForce_local = 0; |
1135 |
> |
|
1136 |
> |
for(int i = 0; i < nAtoms; i++){ |
1137 |
> |
atoms[i]->getFrc(force); |
1138 |
> |
totalForce_local += force[whichDirection]; |
1139 |
> |
} |
1140 |
> |
|
1141 |
> |
#ifndef IS_MPI |
1142 |
> |
totalForce = totalForce_local; |
1143 |
> |
#else |
1144 |
> |
MPI_Allreduce(&totalForce_local, &totalForce, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1145 |
> |
#endif |
1146 |
> |
|
1147 |
> |
return totalForce; |
1148 |
> |
|
1149 |
> |
} |
1150 |
> |
|
1151 |
> |
/** |
1152 |
> |
* |
1153 |
> |
*/ |
1154 |
> |
|
1155 |
> |
template<typename T> void ZConstraint<T>::PolicyByNumber::update(){ |
1156 |
> |
//calculate the number of atoms of moving z-constrained molecules |
1157 |
> |
int nMovingZAtoms_local; |
1158 |
> |
int nMovingZAtoms; |
1159 |
> |
|
1160 |
> |
nMovingZAtoms_local = 0; |
1161 |
> |
for(int i = 0; i < (int)((zconsIntegrator->zconsMols).size()); i++) |
1162 |
> |
if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving)) |
1163 |
> |
nMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getNAtoms(); |
1164 |
> |
|
1165 |
> |
#ifdef IS_MPI |
1166 |
> |
MPI_Allreduce(&nMovingZAtoms_local, &nMovingZAtoms, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
1167 |
> |
#else |
1168 |
> |
nMovingZAtoms = nMovingZAtoms_local; |
1169 |
> |
#endif |
1170 |
> |
totNumOfMovingAtoms = nMovingZAtoms + zconsIntegrator->totNumOfUnconsAtoms; |
1171 |
> |
} |
1172 |
> |
|
1173 |
> |
template<typename T>double ZConstraint<T>::PolicyByNumber::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
1174 |
> |
return totalForce / mol->getNAtoms(); |
1175 |
> |
} |
1176 |
> |
|
1177 |
> |
template<typename T> double ZConstraint<T>::PolicyByNumber::getZFOfMovingMols(Atom* atom, double totalForce){ |
1178 |
> |
return totalForce / totNumOfMovingAtoms; |
1179 |
> |
} |
1180 |
> |
|
1181 |
> |
template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
1182 |
> |
return totalForce / mol->getNAtoms(); |
1183 |
> |
} |
1184 |
> |
|
1185 |
> |
template<typename T> double ZConstraint<T>::PolicyByNumber::getHFOfUnconsMols(Atom* atom, double totalForce){ |
1186 |
> |
return totalForce / zconsIntegrator->totNumOfUnconsAtoms; |
1187 |
> |
} |
1188 |
> |
|
1189 |
> |
/** |
1190 |
> |
* |
1191 |
> |
*/ |
1192 |
> |
|
1193 |
> |
template<typename T> void ZConstraint<T>::PolicyByMass::update(){ |
1194 |
> |
//calculate the number of atoms of moving z-constrained molecules |
1195 |
> |
double massOfMovingZAtoms_local; |
1196 |
> |
double massOfMovingZAtoms; |
1197 |
> |
|
1198 |
> |
massOfMovingZAtoms_local = 0; |
1199 |
> |
for(int i = 0; i < (int)((zconsIntegrator->zconsMols).size()); i++) |
1200 |
> |
if((zconsIntegrator->states)[i] == (zconsIntegrator->zcsMoving)) |
1201 |
> |
massOfMovingZAtoms_local += (zconsIntegrator->zconsMols)[i]->getTotalMass(); |
1202 |
> |
|
1203 |
> |
#ifdef IS_MPI |
1204 |
> |
MPI_Allreduce(&massOfMovingZAtoms_local, &massOfMovingZAtoms, 1, MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1205 |
> |
#else |
1206 |
> |
massOfMovingZAtoms = massOfMovingZAtoms_local; |
1207 |
> |
#endif |
1208 |
> |
totMassOfMovingAtoms = massOfMovingZAtoms + zconsIntegrator->totalMassOfUncons; |
1209 |
> |
} |
1210 |
> |
|
1211 |
> |
template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
1212 |
> |
return totalForce * atom->getMass() / mol->getTotalMass(); |
1213 |
> |
} |
1214 |
> |
|
1215 |
> |
template<typename T> double ZConstraint<T>::PolicyByMass::getZFOfMovingMols( Atom* atom, double totalForce){ |
1216 |
> |
return totalForce * atom->getMass() / totMassOfMovingAtoms; |
1217 |
> |
} |
1218 |
> |
|
1219 |
> |
template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfFixedZMols(Molecule* mol, Atom* atom, double totalForce){ |
1220 |
> |
return totalForce * atom->getMass() / mol->getTotalMass(); |
1221 |
> |
} |
1222 |
> |
|
1223 |
> |
template<typename T> double ZConstraint<T>::PolicyByMass::getHFOfUnconsMols(Atom* atom, double totalForce){ |
1224 |
> |
return totalForce * atom->getMass() / zconsIntegrator->totalMassOfUncons; |
1225 |
> |
} |
1226 |
> |
|